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Calcium in PDB 8ebt: Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)

Enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)

All present enzymatic activity of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5):
3.6.4.12;

Other elements in 8ebt:

The structure of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) also contains other interesting chemical elements:

Zinc (Zn) 6 atoms
Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) (pdb code 8ebt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5), PDB code: 8ebt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8ebt

Go back to Calcium Binding Sites List in 8ebt
Calcium binding site 1 out of 2 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca400

b:504.7
occ:1.00
OD2 J:ASP116 2.6 524.4 1.0
OG1 J:THR118 2.9 515.3 1.0
OD1 J:ASN125 3.3 469.4 1.0
CG2 J:THR118 3.3 515.3 1.0
CG J:ASP116 3.5 524.4 1.0
CB J:THR118 3.5 515.3 1.0
OG J:SER122 3.7 462.0 1.0
OD1 J:ASP116 3.8 524.4 1.0
CG J:ASN125 4.3 469.4 1.0
CB J:SER122 4.4 462.0 1.0
O J:LYS120 4.6 481.8 1.0
ND2 J:ASN125 4.6 469.4 1.0
CB J:ASP116 4.8 524.4 1.0
OD1 J:ASP114 4.8 509.1 1.0
CA J:THR118 4.9 515.3 1.0

Calcium binding site 2 out of 2 in 8ebt

Go back to Calcium Binding Sites List in 8ebt
Calcium binding site 2 out of 2 in the Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xpa Repositioning CORE7 of Tfiih Relative to Xpc-Dna Lesion (CY5) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:469.1
occ:1.00
N J:SER158 2.7 459.1 1.0
OD2 J:ASP154 3.0 466.0 1.0
OE1 J:GLU161 3.0 452.2 1.0
CD J:GLU161 3.0 452.2 1.0
OG J:SER158 3.1 459.1 1.0
CB J:SER158 3.1 459.1 1.0
OE2 J:GLU161 3.2 452.2 1.0
C J:VAL157 3.3 459.7 1.0
CA J:VAL157 3.4 459.7 1.0
O J:GLU156 3.4 463.0 1.0
CA J:SER158 3.5 459.1 1.0
OD1 J:ASP154 3.6 466.0 1.0
CG J:ASP154 3.6 466.0 1.0
OD1 J:ASP152 3.6 464.9 1.0
CG J:GLU161 3.8 452.2 1.0
C J:GLU156 3.9 463.0 1.0
OD2 J:ASP152 3.9 464.9 1.0
N J:VAL157 3.9 459.7 1.0
CG J:ASP152 4.1 464.9 1.0
OD1 J:ASP150 4.3 453.0 1.0
O J:VAL157 4.3 459.7 1.0
CB J:GLU161 4.4 452.2 1.0
CE J:LYS120 4.6 481.8 1.0
CD J:LYS120 4.6 481.8 1.0
CG J:GLU156 4.7 463.0 1.0
C J:SER158 4.7 459.1 1.0
CB J:VAL157 4.8 459.7 1.0

Reference:

J.Kim, C.L.Li, X.Chen, Y.Cui, F.M.Golebiowski, H.Wang, F.Hanaoka, K.Sugasawa, W.Yang. Lesion Recognition By Xpc, Tfiih and Xpa in Dna Excision Repair Nature 2023.
ISSN: ESSN 1476-4687
Page generated: Thu Jul 10 04:04:57 2025

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